Scanning transmission electron microscopy (STEM) has been combined with parallel electron energy-loss spectroscopy (EELS) to develop new techniques that complement conventional electron microscopy-based structural biology. To assess the potential of valence EELS for imaging the distributions of biological compounds in cells, high-resolution spectra have been obtained from specimens of protein, carbohydrate, nucleic acid, and lipids, as well as from vitrified water. Knowledge of these valence spectra can be used to map cellular water distributions in frozen hydrated cryosections. Improved methods have also been developed for quantifying core-edge spectra by correcting for channel-to-channel gain variations and by subtracting the dominant inverse-power background component underlying the core-edges. Spectra have been recorded from well-characterized compounds such as cysteine and ATP, thus allowing relative scattering cross sections to be determined for sulfur, phosphorus, and nitrogen.